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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.24.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-20, 12:09 PST based on data in: /gscratch/scrubbed/sr320/github/ceasmallr/output/04-bismark-align

        General Statistics

        Showing 32/32 rows and 2/3 columns.
        Sample Name% Aligned% Aligned
        CF01-CM01-Zygote_R1_001
        12.8%
        CF01-CM01-Zygote_stderr
        6.5%
        CF01-CM02-Larvae_R1_001
        35.9%
        CF01-CM02-Larvae_stderr
        17.6%
        CF02-CM02-Zygote_R1_001
        13.9%
        CF02-CM02-Zygote_stderr
        5.9%
        CF03-CM03-Zygote_R1_001
        25.6%
        CF03-CM03-Zygote_stderr
        12.0%
        CF03-CM04-Larvae_PE_report
        46.1%
        CF03-CM04-Larvae_stderr
        22.0%
        CF03-CM05-Larvae_PE_report
        34.0%
        CF03-CM05-Larvae_stderr
        16.3%
        CF04-CM04-Zygote_PE_report
        25.1%
        CF04-CM04-Zygote_stderr
        11.2%
        CF05-CM02-Larvae_PE_report
        35.2%
        CF05-CM02-Larvae_stderr
        16.8%
        CF05-CM05-Zygote_PE_report
        25.3%
        CF05-CM05-Zygote_stderr
        13.1%
        CF06-CM01-Zygote_PE_report
        23.5%
        CF06-CM01-Zygote_stderr
        11.3%
        CF06-CM02-Larvae_PE_report
        22.7%
        CF06-CM02-Larvae_stderr
        11.0%
        CF07-CM02-Zygote_PE_report
        11.5%
        CF07-CM02-Zygote_stderr
        5.6%
        CF08-CM03-Zygote_PE_report
        18.9%
        CF08-CM03-Zygote_stderr
        7.9%
        CF08-CM04-Larvae_PE_report
        0.9%
        CF08-CM04-Larvae_stderr
        0.6%
        CF08-CM05-Larvae_PE_report
        2.1%
        CF08-CM05-Larvae_stderr
        1.1%
        EF01-EM01-Zygote_PE_report
        21.9%
        EF01-EM01-Zygote_stderr
        10.8%

        Bismark

        Version: 0.24.2

        Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167

        Alignment Rates

        Created with MultiQC

        Strand Alignment

        Created with MultiQC

        Bowtie 2 / HiSAT2

        Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Paired-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        There are 6 possible types of alignment:

        • PE mapped uniquely: Pair has only one occurence in the reference genome.
        • PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
        • PE one mate mapped uniquely: One read of a pair has one occurence.
        • PE multimapped: Pair has multiple occurence.
        • PE one mate multimapped: One read of a pair has multiple occurence.
        • PE neither mate aligned: Pair has no occurence.
        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bismark0.24.2

        MultiQC v1.24.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.